ISfinder Mirror Site

ISSpma3

Family IS3
Group IS407

MGE type ISRelated element(s) :
Isoform Synonym(s)

Accession number	Transposition	Origin	Host
AB196775	ND	Sphingopyxis macrogoltabida	Sphingopyxis macrogoltabida

DNA section

IS Length : 1269 bp

Ends

IR Length : 33/39

IRL : TGACGTGACCCCCTGATTTTCCTCCAACAGTGATTAGAGTCCGGTCTTGA
IRR : TGACGTGACCCCCTGGTTTCCACCAGCGGGGATTAGAGCCCAGCAGCTTT

Insertion site

Left flank	Direct repeat	Right flank	DR Length
GGGTTTGTGG	CGTG	CTTTCGCACG	4

DNA sequence

TGACGTGACCCCCTGATTTTCCTCCAACAGTGATTAGAGTCCGGTCTTGAAGGAAGGACGGACAGATGAAGCGTTTGAGGTTTTCGGAAGAGCAGATCAT
CGGGGTGTTGAAGGAAGCGGAGGCGGGCGCGAAGACCGGCGAGCTGGCGCGGCGACACGGGGTGTCGGAAGCAACGATCTACAACTGGAAGGCCAAGTAT
GGCGGCCTTGAGGTGTCGGAGGCGAAGCGGCTACGCTCGCTCGAGGACGAGAACGCGAAGCTGAAGCGGTTGCTTGCGGACTCGATGCTGGACAATGCGG
CGCTGAAGGATCTTCTCACAAAAAAATGGTGACGCCCGCCGTTCAGCGGGAAGCGGTCGCCCATCTCCAGGCTTGCCATGGGATGAGCGAGCGGCGGGCG
TGCCGTGTCACAGGCGCCGATCGGAAGAGCATGCGCTACCGGTCGCAGCGTGGCGACGATGCCGAGGTTCGGGAGAAGCTGCGCGAGTTGGCGCAGCAGC
GTCGCCGGTTCGGTTATCGGCGCCTGCATATCCTGCTGCGCCGGGAGGGCGTGATGATCAACAGGAAGAAGACCCAGCGCCTGTATCGAGAGGAGGGGCT
GATGGTCCGACGAAGACGCAACCGGCGCCGGGCGATCGGTGCGCGGGCGCCCGCACCGGTGCTCGCGCTGCCGAACCAGCGGTGGAGCCTCGACTTTGTG
CATGATCAGATGGCGTCAGGTCGGCGGTTCCGGGTGCTCAACATCGTGGACGATGTCACGCGGGAGTGCCTGCGCGCGGTGCCCGACACGTCGATCTCCG
GGCGCCGGGTCGTGCGCGAGCTCAGCGATCTGATCGAGGAGCGCGGCAGACCGGGGATGATCGTCAGCGACAATGGGACCGAGCTGACATCGAACGCGGT
GCTCGCATGGTGCGGTGAGGTCGGGGTCGAGTGGCATTATATCGCGCCGGGCAAGCCGATGCAGAACGGCTATGTCGAGAGCTTCAATGGCCGGATGCGC
GATGAGCTTCTGAACGAGACGCTGTTCCTCGACCTCGATCATGCCCGCACAGTGATCGCGGCCTGGGCCGAAGATTACGACCAGGCGCGGCCACACTCGG
CCCTTGGATATGAGACACCGGCGGCGTTCGCCGCCGAACTGCATAAGCAATGGCCTGTGCAGCTACGCCCTTCGGGCTCCGCTGCACAGGCCATTGCTTA
CACTGCGCTCATGCGCAACAAAGCTGCTGGGCTCTAATCCCCGCTGGTGGAAACCAGGGGGTCACGTCA

Recoding section

Recoding by frameshift
Frame
Type
Experimentally demonstrated

Stimulators :

Shine-Dalgarno sequence :
Secondary structure :

Recoding motif :

Protein section

ORF number : 3

ORF 1

Length		Begin	End	Strand	Fusion ORF
267 bp	88 aa	66	332	+	No

ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MKRLRFSEEQIIGVLKEAEAGAKTGELARRHGVSEATIYNWKAKYGGLEVSEAKRLRSLEDENAKLKRLLADSMLDNAALKDLLTKKW

Blast result :

ORF 2

Length		Begin	End	Strand	Fusion ORF
1026 bp	341 aa	212	1237	+	No

ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

GVGGEAATLARGREREAEAVACGLDAGQCGAEGSSHKKMVTPAVQREAVAHLQACHGMSERRACRVTGADRKSMRYRSQRGDDAEVREKLRELAQQRRRF
GYRRLHILLRREGVMINRKKTQRLYREEGLMVRRRRNRRRAIGARAPAPVLALPNQRWSLDFVHDQMASGRRFRVLNIVDDVTRECLRAVPDTSISGRRV
VRELSDLIEERGRPGMIVSDNGTELTSNAVLAWCGEVGVEWHYIAPGKPMQNGYVESFNGRMRDELLNETLFLDLDHARTVIAAWAEDYDQARPHSALGY
ETPAAFAAELHKQWPVQLRPSGSAAQAIAYTALMRNKAAGL

Blast result :

ORF 3

Length		Begin	End	Strand	Fusion ORF
1172 bp	390 aa	66	1237	+	Yes

ORF function : Transposase
Chemistry : DDE

ORF sequence :

MKRLRFSEEQIIGVLKEAEAGAKTGELARRHGVSEATIYNWKAKYGGLEVSEAKRLRSLEDENAKLKRLLADSMLDNAALKDLLTKKMVTPAVQREAVAH
LQACHGMSERRACRVTGADRKSMRYRSQRGDDAEVREKLRELAQQRRRFGYRRLHILLRREGVMINRKKTQRLYREEGLMVRRRRNRRRAIGARAPAPVL
ALPNQRWSLDFVHDQMASGRRFRVLNIVDDVTRECLRAVPDTSISGRRVVRELSDLIEERGRPGMIVSDNGTELTSNAVLAWCGEVGVEWHYIAPGKPMQ
NGYVESFNGRMRDELLNETLFLDLDHARTVIAAWAEDYDQARPHSALGYETPAAFAAELHKQWPVQLRPSGSAAQAIAYTALMRNKAAGL

Blast result :

Comments

ISSpma3 is 91% aa similar to ISEli1. The third ORF is a putative ORFAB transposase reconstructed in silico by possible -1 frameshift.

References

1] ISfinder annotation (2009)
2] Ohta,T., Tani,A., Kimbara,K. and Kawai,F. (2005) Appl. Microbiol. Biotechnol. 68 (5), 639-646
3] Charoenpanich,J., Tani,A., Moriwaki,N., Kimbara,K. and Kawai,F. (2006) Microbiology (Reading, Engl.) 152 (PT 10), 3025-3034
4] Tani,A., Charoenpanich,J., Mori,T., Takeichi,M., Kimbara,K. and Kawai,F. (2007) Microbiology (Reading, Engl.) 153 (PT 2), 338-346